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    Assaying Thermo-nociceptive Behavior in Drosophila Larvae
    Authors:  Meike Petersen, Federico Tenedini, Nina Hoyer, Fritz Kutschera and Peter Soba, date: 02/20/2018, view: 20, Q&A: 0
    Thermo-nociception, the detection and behavioral response to noxious temperatures, is a highly conserved action to avoid injury and ensure survival. Basic molecular mechanisms of thermal responses have been elucidated in several model organisms and ...
    Assaying Mechanonociceptive Behavior in Drosophila Larvae
    Authors:  Nina Hoyer, Meike Petersen, Federico Tenedini and Peter Soba, date: 02/20/2018, view: 16, Q&A: 0
    Drosophila melanogaster larvae have been extensively used as a model to study the molecular and cellular basis of nociception. The larval nociceptors, class IV dendritic arborization (C4da) neurons, line the body wall of the animal and ...
    A Small RNA Isolation and Sequencing Protocol and Its Application to Assay CRISPR RNA Biogenesis in Bacteria
    Next generation high-throughput sequencing has enabled sensitive and unambiguous analysis of RNA populations in cells. Here, we describe a method for isolation and strand-specific sequencing of small RNA pools from bacteria that can be multiplexed ...
    Adapting the Smart-seq2 Protocol for Robust Single Worm RNA-seq
    Most nematodes are small worms that lack enough RNA for regular RNA-seq protocols without pooling hundred to thousand of individuals. We have adapted the Smart-seq2 protocol in order to sequence the transcriptome of an individual worm. While ...
    Conditional Knockdown of Proteins Using Auxin-inducible Degron (AID) Fusions in Toxoplasma gondii
    Authors:  Kevin M. Brown, Shaojun Long and L. David Sibley, date: 02/20/2018, view: 25, Q&A: 0
    Toxoplasma gondii is a member of the deadly phylum of protozoan parasites called Apicomplexa. As a model apicomplexan, there is a great wealth of information regarding T. gondii’s 8,000+ protein coding genes including sequence ...
    An Improved Method for Measuring Chromatin-binding Dynamics Using Time-dependent Formaldehyde Crosslinking
    Formaldehyde crosslinking is widely used in combination with chromatin immunoprecipitation (ChIP) to measure the locations along DNA and relative levels of transcription factor (TF)-DNA interactions in vivo. However, the measurements that ...
    Transient Gene Expression for the Characteristic Signal Sequences and the Estimation of the Localization of Target Protein in Plant Cell
    We have proposed and tested a method for characterization of the signal sequences and determinations of target protein localization in a plant cell. This method, called the AgI-PrI, implies extraction of protoplasts from plant tissues after ...
    Assaying Thermo-nociceptive Behavior in Drosophila Larvae
    Authors:  Meike Petersen, Federico Tenedini, Nina Hoyer, Fritz Kutschera and Peter Soba, date: 02/20/2018, view: 20, Q&A: 0
    [Abstract] Thermo-nociception, the detection and behavioral response to noxious temperatures, is a highly conserved action to avoid injury and ensure survival. Basic molecular mechanisms of thermal responses have been elucidated in several model organisms and are of clinical relevance as thermal hypersensitivity (thermos-allodynia) is common in neuropathic ...
    Assaying Mechanonociceptive Behavior in Drosophila Larvae
    Authors:  Nina Hoyer, Meike Petersen, Federico Tenedini and Peter Soba, date: 02/20/2018, view: 16, Q&A: 0
    [Abstract] Drosophila melanogaster larvae have been extensively used as a model to study the molecular and cellular basis of nociception. The larval nociceptors, class IV dendritic arborization (C4da) neurons, line the body wall of the animal and respond to various stimuli including noxious heat and touch. Activation of C4da neurons results in a ...
    A Small RNA Isolation and Sequencing Protocol and Its Application to Assay CRISPR RNA Biogenesis in Bacteria
    [Abstract] Next generation high-throughput sequencing has enabled sensitive and unambiguous analysis of RNA populations in cells. Here, we describe a method for isolation and strand-specific sequencing of small RNA pools from bacteria that can be multiplexed to accommodate multiple biological samples in a single experiment. Small RNAs are isolated by ...
    Adapting the Smart-seq2 Protocol for Robust Single Worm RNA-seq
    [Abstract] Most nematodes are small worms that lack enough RNA for regular RNA-seq protocols without pooling hundred to thousand of individuals. We have adapted the Smart-seq2 protocol in order to sequence the transcriptome of an individual worm. While developed for individual Steinernema carpocapsae and Caenorhabditis elegans larvae as ...
    Conditional Knockdown of Proteins Using Auxin-inducible Degron (AID) Fusions in Toxoplasma gondii
    Authors:  Kevin M. Brown, Shaojun Long and L. David Sibley, date: 02/20/2018, view: 25, Q&A: 0
    [Abstract] Toxoplasma gondii is a member of the deadly phylum of protozoan parasites called Apicomplexa. As a model apicomplexan, there is a great wealth of information regarding T. gondii’s 8,000+ protein coding genes including sequence variation, expression, and relative contribution to parasite fitness. However, new tools are needed to ...
    An Improved Method for Measuring Chromatin-binding Dynamics Using Time-dependent Formaldehyde Crosslinking
    [Abstract] Formaldehyde crosslinking is widely used in combination with chromatin immunoprecipitation (ChIP) to measure the locations along DNA and relative levels of transcription factor (TF)-DNA interactions in vivo. However, the measurements that are typically made do not provide unambiguous information about the dynamic properties of these ...
    Transient Gene Expression for the Characteristic Signal Sequences and the Estimation of the Localization of Target Protein in Plant Cell
    [Abstract] We have proposed and tested a method for characterization of the signal sequences and determinations of target protein localization in a plant cell. This method, called the AgI-PrI, implies extraction of protoplasts from plant tissues after agroinfiltration. The suggested approach combines the advantages of two widely used methods for transient ...
    Immunoprecipitation of Tri-methylated Capped RNA
    Authors:  Karen E. Hayes, Jamie A. Barr, Mingyi Xie, Joan A. Steitz and Ivan Martinez, date: 02/05/2018, view: 156, Q&A: 0
    [Abstract] Cellular quiescence (also known as G0 arrest) is characterized by reduced DNA replication, increased autophagy, and increased expression of cyclin-dependent kinase p27Kip1. Quiescence is essential for wound healing, organ regeneration, and preventing neoplasia. Previous findings indicate that microRNAs (miRNAs) play an ...
    Measuring Nucleosome Assembly Activity in vitro with the Nucleosome Assembly and Quantification (NAQ) Assay
    Authors:  Francesca Mattiroli, Yajie Gu and Karolin Luger, date: 02/05/2018, view: 135, Q&A: 0
    [Abstract] Nucleosomes organize the eukaryotic genome into chromatin. In cells, nucleosome assembly relies on the activity of histone chaperones, proteins with high binding affinity to histones. At least a subset of histone chaperones promotes histone deposition in vivo. However, it has been challenging to characterize this activity, due to the lack ...
    Determination of DNA Damage in the Retina Photoreceptors of Drosophila
    Authors:  Damulewicz Milena and Pyza Elzbieta, date: 02/05/2018, view: 86, Q&A: 0
    [Abstract] The retina is sensitive for light damages, because of direct light exposure, especially intense blue and UV light, which increase level of ROS and other toxic phototransduction products in photoreceptor cells. In our previous work (Damulewicz et al., 2017a and 2017b), we used 8-oxo-deoxyguanosine (8-OHdG) as a marker for oxidative stress ...